Evolution of diversity in epidemics revealed by analysis of the human bacterial pathogen group A Streptococcus

► Genomic, transcriptomic and proteomic study of 4 closely related GAS strains. ► Small number of genetic changes result in large variation in transcriptome/proteome. ► Intergenic polymorphisms most frequently associate with cis transcription changes. ► Polymorphisms in ropB correspond with reduced expression and production of SpeB. ► Reduced SpeB coincides with increased levels of certain secreted virulence factors.